SAXSdb — 9p1i

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Actin, cytoplasmic 1

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	VopV × 12 （A0A250E4R0） MAGNESIUM ION × 12 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 12 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ACTB_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain Q； PDBConstruct 1–375； UniProt 1–375 Author chain R； PDBConstruct 1–375； UniProt 1–375 Author chain S； PDBConstruct 1–375； UniProt 1–375 Author chain T； PDBConstruct 1–375； UniProt 1–375 Author chain U； PDBConstruct 1–375； UniProt 1–375 Author chain V； PDBConstruct 1–375； UniProt 1–375 Author chain W； PDBConstruct 1–375； UniProt 1–375 Author chain X； PDBConstruct 1–375； UniProt 1–375 Author chain Y； PDBConstruct 1–375； UniProt 1–375 Author chain Z； PDBConstruct 1–375； UniProt 1–375 Author chain a； PDBConstruct 1–375； UniProt 1–375 Author chain b； PDBConstruct 1–375； UniProt 1–375

VopV

Vibrio parahaemolyticus

UniProt A0A250E4R0

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 24	Actin, cytoplasmic 1 × 12 （P60709） MAGNESIUM ION × 12 PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 12 water × 12	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	A0A250E4R0_VIBPH
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain c； PDBConstruct 1–2402； UniProt 1–2402 Author chain d； PDBConstruct 1–2402； UniProt 1–2402 Author chain e； PDBConstruct 1–2402； UniProt 1–2402 Author chain f； PDBConstruct 1–2402； UniProt 1–2402 Author chain g； PDBConstruct 1–2402； UniProt 1–2402 Author chain h； PDBConstruct 1–2402； UniProt 1–2402 Author chain i； PDBConstruct 1–2402； UniProt 1–2402 Author chain j； PDBConstruct 1–2402； UniProt 1–2402 Author chain k； PDBConstruct 1–2402； UniProt 1–2402 Author chain l； PDBConstruct 1–2402； UniProt 1–2402 Author chain m； PDBConstruct 1–2402； UniProt 1–2402 Author chain n； PDBConstruct 1–2402； UniProt 1–2402

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9p1i
Deposition date deposition_date	2025-06-10
Structure title title	Atomic structure of vibrio effector fragment VopV bound to Beta-cytoplasmic/gamma1-cytoplasmic F-actin
Keywords keywords	actin, Vibrio, effector proteins, T3SS, cryo-EM, actin isoforms, STRUCTURAL PROTEIN; STRUCTURAL PROTEIN
Experimental Method method	ELECTRON MICROSCOPY

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

9p1i__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

9p1i__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9p1i__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	94.86 Å
Rg (electron density)	98.55 Å
Total Rg	98.02 Å
Atom count	39612
Residues	5016
Excluded volume	703560 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9p1i__assembly_1__model_1`	24-meric （24）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Actin, cytoplasmic 1
Molecular weight formula_weight	41795.7 kDa
EC 编号 ec_number	3.6.4.-
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	Q,R,S,T,U,V,W,X,Y,Z,a,b
Atom count atom_count	39624

MDDDIAALVVDNGSGMCKAGFAGDDAPRAVFPSIVGRPRHQGVMVGMGQKDSYVGDEAQSKRGILTLKYPIEHGIVTNWDDMEKIWHHTFYNELRVAPEEHPVLLTEAPLNPKANREKMTQIMFETFNTPAMYVAIQAVLSLYASGRTTGIVMDSGDGVTHTVPIYEGYALPHAILRLDLAGRDLTDYLMKILTERGYSFTTTAEREIVRDIKEKLCYVALDFEQEMATAASSSSLEKSYELPDGQVITIGNERFRCPEALFQPSFLGMESCGIHETTFNSIMKCDVDIRKDLYANTVLSGGTTMYPGIADRMQKEITALAPSTMKIKIIAPPERKYSVWIGGSILASLSTFQQMWISKQEYDESGPSIVHRKCF

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Komagataella pastoris

Entity 2 Entity 2 polymer

Description description	VopV
Molecular weight formula_weight	244355.4 kDa
Source method src_method	man
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	c,d,e,f,g,h,i,j,k,l,m,n

MINSLNIQNTGSISELGQSPNLTINSAPAPSVLPRSEALANSNDVLPSAVTAQDSCFEQGEEKLTENNNVNKPAKNKKVNCKSNKYNNKTKAKTHLAAIAGATTLGAVLAPFTGGLSLLPTAFVVLFGNASALAMYGGSEFFLGQNAINKEEVPKDKLKEKETPETALKRTPERPIFPRYLERRTHFDEVDGLKRNGPDSFNVTNNYYSPTFNINVGDYFFNNQTNNRDESKAEDKPFAESAAQSDVSSQTTTLFDEAIQNMGQLQVVDVSEISPDTLFSEVTDHATNIGTEDTVDNLLGALESCHLQSGQAKLVKVTLEGGLQAYLGGISDDTADALPPVVTENVTSSPVKKWPEVKIPARIITTSGNASVDGNPGYRPTRVDSNGETMGYEMRDRVSSSSTPSQSTATSSKGSVNTERSATQTGTPAQADSTKGVEPNVSTPEQKPSADASNGEPTSVQGKTSEGIDSGVGTPESTPSMDAATGEPNTADDKHAVGESTPTHESGESVASVESEPASSGPAKRWPEVKTPARVITSAGNASVDGNPGYRPTRVDSNGETMGYEMRDRVSSSSTPSPSTAPSSKGSVNAEGNAPQTGTPAQAGSSKGVEPNVATPEQKPSADVSSGEPTSAQGNASEGIDSGVATPEQKPSADAFSGEPTSAQGNASEGIDAGVATPEQKPSMGASSGEPTSAQGNASEGTDSGVGTPESTPSVDAATGEPNTADDKNAVGESTPTHESGESVPSVESEQASSGPAKRWPEVKTPARVITSAGNASIDGNPGYRPTRVDSNGETMGYEMRDRVPASSTPSASTGPSSKGSVNAEGNAPQTGTPAQAGSSKGVEPNVATPEQKPSADASSGEPTAAQGNASEGIDSGVGTPESTPSVDAATGEPNTADDKNAVGESTPTHESGESVPSVESEQASSGPAKRWPEVKTPARVITSAGNASIDGNPGYRPTRVDSNGETMGYEMRDRVPASSTPSPSSAPSSNGSVNAEGNAPQTGTPTQAGSSNVEPSVATPEQKPSADASSGEPISTQGNAPESIDSGVATPEQKPSAEASSGEPTSAQGNASEGIDSGVDTPESTPSVDAATGEPNTADNKNAAGESTPSVEPEQAPSGPAKRWPEVKTPARVITSAGNASIDGNPGYRPTRVDSNGETMGYEMRDRVPASSTPSASTAPSSKGSVNAEGNAPQTGTPAQAGSANVEPKVATPEQKTSADVSRGEPTLTQGNAPEGIDSGVATPEQKPSVSGSTDEPTLAQGNAPEGIDAGVSTPESTPSVDAATGEPNTADDKNAAGESIPTLAEGATPTHESGESVPSVEPEQTSSGPAKRWPEVKTPARVITSAGNASIDGNPGYRPTRVDSNGETMGYEMRDRVPASSTPSASTAASSKGSVNAEGNAPQTGTPAQAGSSNVEPSVATPEQKPSADAFSGEPTSAQGNAPEGIDAGVSTPESTPSVDAATGEPNTADDKNAAGESIPTLAEGATPTHESGESVPSVEPEQTSSGPAKRWPEVKTPARVITSAGNASIDGNPGYRPTRVDSNGETMGYEMRDRVPASSTPSASTAASSKGSVNAEGNAPQTGTPAQAGSSNVEPSVATPEQKPSVSGSTDEPTLAQGNASEGIDAGVSTPESTPSVDAATGEPNTADNKNAAGESIPTLAEGATPTHESGESVPSVEPEQTSSGPAKRWPEVKTPARVITSAGNASIDGNPGYRPTRVDSNGETMGYEMRDRVPASSTPSASTAASSKGSVNAEGNAPQTGTPAQAGSSNVEPSVATPEQKPSADAFSGEPTSAQGNAPEGIDAGVSTPESTPSVDAATGEPNTADDKNAAGESIPTLAEGATPTHESGESVPSVEPEQTSSGPAKRWPEVKTPARVITSAGNASIDGNPGYRPTRVDSNGETMGYEMRDRVPASSTPSASTAASSKGSVNAEGNAPQTGTPAQAGSSNVEPSVATPEQKPSVSGSTDEPTLAQGNASEGIDAGVSTPESTPSVDAATGEPNTADNKNAVGESSPTHESGESVPSVEPEQTSSGPAKRWPEVKTPARVITSAGNASIDGNPGYRPTRVDSNGETMGYEMRDRVPASSTPSASTAASSKGSVNAEGNAPQTGTPAQAGSSNVEPSVATPEQKPSADAFSGEPTSAQGNAPEGIDAGVSTPESTPSVDEVNHLATSQEKEVSESSFTHRSEIKFHVNAEIDTDINPLGERFTSTLKVNLGSGQASIQTQASDSFVDWQSAQVEDGIEFKEAVLVTEDVKDEILWATGELNDGPELRFAKKIDNSSAQNFESGLDNQRTASSGVARNEGSTKEVVGSVSGKKWKVNMPAPVLTTQGMMSGHARNYTQGILNNIRDLNTTRKEYETTLVSGLVGSNSSVSIWAHSERSMVVPVANSSNFKMM

Source Source

Source organism organism	Vibrio parahaemolyticus
NCBI taxonomy ID ncbi_taxonomy_id	670
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 4 Entity 4 non-polymer

Description description	PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Molecular weight formula_weight	506.2 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

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Resolution resolution	3.00 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	140672

Atomic structure of vibrio effector fragment VopV bound to Beta-cytoplasmic/gamma1-cytoplasmic F-actin

1. Protein Identity and Related Structures Protein Identity & Related Structures

Actin, cytoplasmic 1

State in the Current Structure

Other States of the Same Protein in the Database

VopV

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9p1i__assembly_1__model_1

9p1i__assembly_1__model_1 | I(q)

9p1i__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)

Atomic structure of vibrio effector fragment VopV bound to Beta-cytoplasmic/gamma1-cytoplasmic F-actin

1. Protein Identity and Related Structures Protein Identity & Related Structures

Actin, cytoplasmic 1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

VopV

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

9p1i__assembly_1__model_1

9p1i__assembly_1__model_1 | I(q)

9p1i__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

7. Citations (1)